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Phil Sci journal: Special section on understanding viruses

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Are they or are they not life forms? Note that the article on giant viruses, abstracted below, is public access.

Studies in History and Philosophy of Science:

Special section on Understanding viruses: Philosophical investigations

For example,

Understanding viruses: Philosophical investigations: Viruses have been virtually absent from philosophy of biology. In this editorial introduction, we explain why we think viruses are philosophically important. We focus on six issues (the definition of viruses, the individuality and diachronic identity of a virus, the possibility to classify viruses into species, the question of whether viruses are living, the question of whether viruses are organisms, and finally the biological roles of viruses in ecology and evolution), and we show how they relate to classic questions of philosophy of biology and even general philosophy. (paywall)

The ecological virus: Ecology is usually described as the study of organisms interacting with one another and their environments. From this view of ecology, viruses – not usually considered to be organisms – would merely be part of the environment. Since the late 1980s, however, a growing stream of micrographic, experimental, molecular, and model-based (theoretical) research has been investigating how and why viruses should be understood as ecological actors of the most important sort. Viruses, especially phage, have been revealed as participants in the planet’s most crucial food webs, even though viruses technically consume nothing (they do not metabolize by themselves). Even more impressively, viruses have been identified as regulators of planetary biogeochemistry, in which they control cycles such as carbon, nitrogen and phosphorus – cycles on which all life depends. Although much biogeochemical research black-boxes the entities filling functional roles, it is useful to focus a little more closely to understand how viruses can be held responsible for the global processes of life. This paper will give a brief overview of the history of virus ecology and tease out the implications of large-scale ecological modelling with viruses. This analysis suggests that viruses should be conceptualized as ecological actors that are at least comparable and possibly equal to organismal actors. Ecological agency can therefore be distinguished from standard interpretations of biological agency. (paywall)

Giant viruses: The difficult breaking of multiple epistemological barriers: The discovery of the first “giant virus”, Mimivirus, in 2003 could solely have been that of an exceptional freak, a blind alley of evolution as occasionally encountered in biology, albeit without conceptual significance. On the contrary, once broken this epistemological barrier, additional unrelated families of giant viruses such as the Pandoraviruses, the Pithoviruses and most recently Mollivirus, were quickly unraveled, suggesting that an entire chapter of microbiology had been ignored since Pasteur and Ivanovski. In this article, we examine to what extent the giant viruses challenge previous definitions of viruses, the diversity of forms they could take, and how they might have evolved from extinct ancestral cellular lineages. Inspired by the epistemology of Gaston Bachelard, we will also suggest the reasons for which giant viruses laid hidden in plain sight for more than a century. Finally, we propose a new definition for “viruses” that paradoxically emphasize the fact that they do not encode a single universally shared macromolecule or biochemical function. (public access)

To be or not to be alive: How recent discoveries challenge the traditional definitions of viruses and life: Three major discoveries have recently profoundly modified our perception of the viral world: molecular ecologists have shown that viral particles are more abundant than cells in natural environments; structural biologists have shown that some viruses from the three domains of life, Bacteria, Eukarya and Archaea, are evolutionarily related, and microbiologists have discovered giant viruses that rival with cells in terms of size and gene content. I discuss here the scientific and philosophical impact of these discoveries on the debates over the definition, nature (living or not), and origin of viruses. I suggest that viruses have often been considered non-living, because they are traditionally assimilated to their virions. However, the term virus describes a biological process and should integrate all aspects of the viral reproduction cycle. It is especially important to focus on the intracellular part of this cycle, the virocell, when viral information is actively expressed and reproduced, allowing the emergence of new viral genes. The virocell concept theoretically removes roadblocks that prevent defining viruses as living organisms. However, defining a “living organism” remains challenging, as indicated by the case of organelles that evolved from intracellular bacteria. To bypass this problem, I suggest considering that all biological entities that actively participate in the process of life are living. (paywall)

The metaphor that viruses are living is alive and well, but it is no more than a metaphor: Virologists often use anthropomorphic metaphors to vividly describe the properties of viruses and this has led some virologists to claim that viruses are living microorganisms. The discovery of giant viruses that are larger and have a more complex genome than small bacteria has fostered the interpretation that viral factories, which are the compartments in virus-infected cells where the virus is being replicated, are able to transform themselves into a new type of living viral organism called a virocell. However, because of the widespread occurrence of horizontal gene transfer, endosymbiosis and hybridization in the evolution of viral genomes, it has not been possible to include metaphorical virocells in the so-called Tree of Life which itself is a metaphor. In the case of viruses that cause human diseases, the infection process is usually presented metaphorically as a war between host and virus and it is assumed that a virus such as the human immunodeficiency virus (HIV) is able to develop new strategies and mechanisms for escaping protective host immune responses. However, the ability of the virus to defeat the immune system is solely due to stochastic mutations arising from the error-prone activity of the viral enzyme reverse transcriptase. The following two types of metaphors will be distinguished: an intentionality metaphor commonly used for attributing goals and intentions to organisms and the living virus metaphor that considers viruses to be actually living organisms. (paywall)

Are viruses alive? The replicator paradigm sheds decisive light on an old but misguided question: The question whether or not “viruses are alive” has caused considerable debate over many years. Yet, the question is effectively without substance because the answer depends entirely on the definition of life or the state of “being alive” that is bound to be arbitrary. In contrast, the status of viruses among biological entities is readily defined within the replicator paradigm. All biological replicators form a continuum along the selfishness-cooperativity axis, from the completely selfish to fully cooperative forms. Within this range, typical, lytic viruses represent the selfish extreme whereas temperate viruses and various mobile elements occupy positions closer to the middle of the range. Selfish replicators not only belong to the biological realm but are intrinsic to any evolving system of replicators. No such system can evolve without the emergence of parasites, and moreover, parasites drive the evolution of biological complexity at multiple levels. The history of life is a story of parasite-host coevolution that includes both the incessant arms race and various forms of cooperation. All organisms are communities of interacting, coevolving replicators of different classes. A complete theory of replicator coevolution remains to be developed, but it appears likely that not only the differentiation between selfish and cooperative replicators but the emergence of the entire range of replication strategies, from selfish to cooperative, is intrinsic to biological evolution. (paywall)

What roles for viruses in origin of life scenarios?: Important roles in origin of life (OL) scenarios have been and still are attributed to viruses. Yet the strict dependence of viruses on cells for their multiplication has been widely acknowledged since the first decades of the 20th century. How could viruses play critical roles in the OL if life relies on cellular organization and if viruses are defined as parasites of cells? In other words, how could viruses play a role in the emergence of cellular life if the existence of cells is a prerequisite for the existence of viruses? This paper investigates this issue and describes past and current OL scenarios conferring viruses with important roles, thereby completing the work of historian of science and physician Scott Podolsky who identified three major roles of viruses in past OL scenarios. Some objections raised by present OL scenarios conferring viruses with an important role are discussed. I argue that disagreements concerning the roles of viruses in OL scenarios stem from the different concepts of life and of virus scientists defend. Investigating the roles of viruses in OL scenarios not only helps identifying different ways to define life in the context of OL theorizing. It also offers the opportunity to better understand how viruses could be conceptualized. The relevance of the replication-first versus metabolism-first dichotomy in OL theorizing is briefly discussed. (paywall)

Writing the history of virology in the twentieth century: Discovery, disciplines, and conceptual change: Concerned with the study of viruses and the diseases they cause, virology is now a well-established scientific discipline. Whereas aspects of its history from the late nineteenth to the mid-twentieth century have often been recounted through a number of detailed case studies, few general discussions of the historiography of virology have been offered. Looking at the ways in which the history of virology has been told, this article examines a number of debates among scientists and historians of biology and show how they are based on a different understanding of notions such as “discipline”, of processes such as “scientific discovery” as well as on distinct views about what the history of science is and how it should be written (the opposition between “longue durée” and “micro-history” or between history of “concepts” versus “experimental methods”). The analysis provided here also suggests that a richer historiography of virology will require looking at the variations over time of the relations between conceptual, technological, and institutional factors that fostered its development at the intersection of several other scientific fields in the life sciences. (paywall) More.

See also: Do some viruses meet the definition of being alive? A teapot is not alive. How do we know it is not? It meets none of the criteria for being alive. No one would consider such a notion. But viruses meet some of the criteria for being alive. Would an accurate understanding of viruses help us with the origin and evolution of life?

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